Publications

Learning Neural Generative Dynamics for Molecular Conformation Generation

Shitong Luo

Jian Peng

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamic… (see more)s, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collection of conformation data. Challenges arise from the limited model capacity for capturing complex distributions of conformations and the difficulty in modeling long-range dependencies between atoms. Inspired by the recent progress in deep generative models, in this paper, we propose a novel probabilistic framework to generate valid and diverse conformations given a molecular graph. We propose a method combining the advantages of both flow-based and energy-based models, enjoying: (1) a high model capacity to estimate the multimodal conformation distribution; (2) explicitly capturing the complex long-range dependencies between atoms in the observation space. Extensive experiments demonstrate the superior performance of the proposed method on several benchmarks, including conformation generation and distance modeling tasks, with a significant improvement over existing generative models for molecular conformation sampling.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

Learning Robust State Abstractions for Hidden-Parameter Block MDPS

2021-05-02

International Conference on Learning Representations (Poster)

openreview.net

Learning Task Decomposition with Ordered Memory Policy Network

Yuchen Lu

Yikang Shen

Siyuan Zhou

Aaron Courville

Joshua B. Tenenbaum

Chuang Gan

Many complex real-world tasks are composed of several levels of sub-tasks. Humans leverage these hierarchical structures to accelerate the l… (see more)earning process and achieve better generalization. In this work, we study the inductive bias and propose Ordered Memory Policy Network (OMPN) to discover subtask hierarchy by learning from demonstration. The discovered subtask hierarchy could be used to perform task decomposition, recovering the subtask boundaries in an unstruc-tured demonstration. Experiments on Craft and Dial demonstrate that our modelcan achieve higher task decomposition performance under both unsupervised and weakly supervised settings, comparing with strong baselines. OMPN can also bedirectly applied to partially observable environments and still achieve higher task decomposition performance. Our visualization further confirms that the subtask hierarchy can emerge in our model.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

Neural Approximate Sufficient Statistics for Implicit Models

Yanzhi Chen

Dinghuai Zhang

Michael U. Gutmann

Aaron Courville

Zhanxing Zhu

We consider the fundamental problem of how to automatically construct summary statistics for implicit generative models where the evaluation… (see more) of the likelihood function is intractable, but sampling data from the model is possible. The idea is to frame the task of constructing sufficient statistics as learning mutual information maximizing representations of the data with the help of deep neural networks. The infomax learning procedure does not need to estimate any density or density ratio. We apply our approach to both traditional approximate Bayesian computation and recent neural likelihood methods, boosting their performance on a range of tasks.

2021-05-02

International Conference on Learning Representations (Spotlight)

doi.org

openreview.net

Predicting Infectiousness for Proactive Contact Tracing

Prateek Gupta

Nasim Rahaman

Pierre-Luc St-Charles

Hannah Alsdurf

Olexa Bilanuik

David Buckeridge

Gaétan Marceau Caron

Pierre-Luc Carrier

Joumana Ghosn

Satya Ortiz-Gagné

Chris Pal

Irina Rish

Bernhard Schölkopf … (see 3 more)

Abhinav Sharma

Jian Tang

Andrew Williams

The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdo… (see more)wns for emergency containment. Large-scale digital contact tracing (DCT) has emerged as a potential solution to resume economic and social activity while minimizing spread of the virus. Various DCT methods have been proposed, each making trade-offs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or pre-existing medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). We find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe re-opening and second-wave prevention.

2021-05-02

International Conference on Learning Representations (Spotlight)

doi.org

openreview.net

Recurrent Independent Mechanisms

Sergey Levine

Bernhard Schölkopf

Learning modular structures which reflect the dynamics of the environment can lead to better generalization and robustness to changes which … (see more)only affect a few of the underlying causes. We propose Recurrent Independent Mechanisms (RIMs), a new recurrent architecture in which multiple groups of recurrent cells operate with nearly independent transition dynamics, communicate only sparingly through the bottleneck of attention, and are only updated at time steps where they are most relevant. We show that this leads to specialization amongst the RIMs, which in turn allows for dramatically improved generalization on tasks where some factors of variation differ systematically between training and evaluation.

2021-05-02

International Conference on Learning Representations (Spotlight)

doi.org

openreview.net

Reinforcement Learning with Random Delays

Christopher Pal

Action and observation delays commonly occur in many Reinforcement Learning applications, such as remote control scenarios. We study the ana… (see more)tomy of randomly delayed environments, and show that partially resampling trajectory fragments in hindsight allows for off-policy multi-step value estimation. We apply this principle to derive Delay-Correcting Actor-Critic (DCAC), an algorithm based on Soft Actor-Critic with significantly better performance in environments with delays. This is shown theoretically and also demonstrated practically on a delay-augmented version of the MuJoCo continuous control benchmark.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

RNNLogic: Learning Logic Rules for Reasoning on Knowledge Graphs

Meng Qu

Junkun Chen

Louis-Pascal Xhonneux

Yoshua Bengio

Jian Tang

This paper studies learning logic rules for reasoning on knowledge graphs. Logic rules provide interpretable explanations when used for pred… (see more)iction as well as being able to generalize to other tasks, and hence are critical to learn. Existing methods either suffer from the problem of searching in a large search space (e.g., neural logic programming) or ineffective optimization due to sparse rewards (e.g., techniques based on reinforcement learning). To address these limitations, this paper proposes a probabilistic model called RNNLogic. RNNLogic treats logic rules as a latent variable, and simultaneously trains a rule generator as well as a reasoning predictor with logic rules. We develop an EM-based algorithm for optimization. In each iteration, the reasoning predictor is first updated to explore some generated logic rules for reasoning. Then in the E-step, we select a set of high-quality rules from all generated rules with both the rule generator and reasoning predictor via posterior inference; and in the M-step, the rule generator is updated with the rules selected in the E-step. Experiments on four datasets prove the effectiveness of RNNLogic.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

Saliency Is a Possible Red Herring When Diagnosing Poor Generalization

Joseph D. Viviano

Becks Simpson

Francis Dutil

Yoshua Bengio

Joseph Paul Cohen

Poor generalization is one symptom of models that learn to predict target variables using spuriously-correlated image features present only … (see more)in the training distribution instead of the true image features that denote a class. It is often thought that this can be diagnosed visually using attribution (aka saliency) maps. We study if this assumption is correct. In some prediction tasks, such as for medical images, one may have some images with masks drawn by a human expert, indicating a region of the image containing relevant information to make the prediction. We study multiple methods that take advantage of such auxiliary labels, by training networks to ignore distracting features which may be found outside of the region of interest. This mask information is only used during training and has an impact on generalization accuracy depending on the severity of the shift between the training and test distributions. Surprisingly, while these methods improve generalization performance in the presence of a covariate shift, there is no strong correspondence between the correction of attribution towards the features a human expert has labelled as important and generalization performance. These results suggest that the root cause of poor generalization may not always be spatially defined, and raise questions about the utility of masks as "attribution priors" as well as saliency maps for explainable predictions.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

Saliency Is a Possible Red Herring When Diagnosing Poor Generalization

Joseph D. Viviano

Becks Simpson

Francis Dutil

Yoshua Bengio

Joseph Paul Cohen

Poor generalization is one symptom of models that learn to predict target variables using spuriously-correlated image features present only … (see more)in the training distribution instead of the true image features that denote a class. It is often thought that this can be diagnosed visually using attribution (aka saliency) maps. We study if this assumption is correct. In some prediction tasks, such as for medical images, one may have some images with masks drawn by a human expert, indicating a region of the image containing relevant information to make the prediction. We study multiple methods that take advantage of such auxiliary labels, by training networks to ignore distracting features which may be found outside of the region of interest. This mask information is only used during training and has an impact on generalization accuracy depending on the severity of the shift between the training and test distributions. Surprisingly, while these methods improve generalization performance in the presence of a covariate shift, there is no strong correspondence between the correction of attribution towards the features a human expert has labelled as important and generalization performance. These results suggest that the root cause of poor generalization may not always be spatially defined, and raise questions about the utility of masks as "attribution priors" as well as saliency maps for explainable predictions.

2021-05-02

International Conference on Learning Representations (Poster)

doi.org

openreview.net

Spatially Structured Recurrent Modules

Nasim Rahaman

Anirudh Goyal

Muhammad Waleed Gondal

Manuel Wuthrich

Stefan Bauer

Yash Sharma

Yoshua Bengio

Bernhard Schölkopf

Capturing the structure of a data-generating process by means of appropriate inductive biases can help in learning models that generalise we… (see more)ll and are robust to changes in the input distribution. While methods that harness spatial and temporal structures find broad application, recent work has demonstrated the potential of models that leverage sparse and modular structure using an ensemble of sparingly interacting modules. In this work, we take a step towards dynamic models that are capable of simultaneously exploiting both modular and spatiotemporal structures. To this end, we model the dynamical system as a collection of autonomous but sparsely interacting sub-systems that interact according to a learned topology which is informed by the spatial structure of the underlying system. This gives rise to a class of models that are well suited for capturing the dynamics of systems that only offer local views into their state, along with corresponding spatial locations of those views. On the tasks of video prediction from cropped frames and multi-agent world modelling from partial observations in the challenging Starcraft2 domain, we find our models to be more robust to the number of available views and better capable of generalisation to novel tasks without additional training than strong baselines that perform equally well or better on the training distribution.

2021-05-02

International Conference on Learning Representations (Poster)

openreview.net